TriGORank: A Gene Ontology Enriched Learning-to-Rank Framework for Trigenic Fitness Prediction

Labhishetty, Sahiti; Lourentzou, Ismini; Volk, Michael Jeffrey; Mishra, Shekhar; Zhao, Huimin; Zhai, Chengxiang

doi:10.1109/bibm52615.2021.9669503

Title: TriGORank: A Gene Ontology Enriched Learning-to-Rank Framework for Trigenic Fitness Prediction

Conference · Thu Dec 09 00:00:00 EST 2021 · 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)

DOI:https://doi.org/10.1109/bibm52615.2021.9669503· OSTI ID:1902720

Labhishetty, Sahiti ^[1]; Lourentzou, Ismini ^[2]; Volk, Michael Jeffrey ^[1]; Mishra, Shekhar ^[1]; Zhao, Huimin ^[1]; Zhai, Chengxiang ^[1]

Univ. of Illinois at Urbana-Champaign, IL (United States)
Univ. of Illinois at Urbana-Champaign, IL (United States); Virginia Polytechnic Inst. and State Univ. (Virginia Tech), Blacksburg, VA (United States)

Machine learning (ML) has been gaining interest in the metabolic engineering community as a means to automate prediction tasks. In this work, we introduce and study the task of using ML to recommend high-fitness triplet mutants as candidates for wet-lab experiments. We first utilize individual fitness and digenic fitness scores as features and train machine learning models that produce a ranked list, from high to low fitness scores, for triplet gene mutants of S. cerevisiae. Then, we incorporate prior metabolic knowledge from an existing gene ontology, by designing a novel graph representation and deducing features that can capture gene similarity and gene interactions. Lastly, experimental results show that our proposed gene ontology enriched model, termed TriGORank, improves both performance and explainability.

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Research Organization:: Univ. of Illinois at Urbana-Champaign, IL (United States)

Sponsoring Organization:: USDOE

DOE Contract Number:: SC0018420

OSTI ID:: 1902720

Journal Information:: 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Conference: 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Houston, TX (United States), 9-12 Dec 2021

Country of Publication:: United States

Language:: English

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